<html>
<body style="padding:20px;width:650px;">
<title>Filter Clusters</title>
<h2>Filter Clusters</h2>
A cluster must pass ALL filters. Beware, it is easy to forget to unset a filter, so execute Clear
to clear all filters in order to start a brand new filter.
<h3>Basic</h3>
<ul>
<li>Filter on cluster ID, Best Hit ID or Description. 
</ul>
<h3>Cluster Info</h3>
<ul>
<li>Filter on Taxa type, which is an
indicator of the composition of the cluster, where mx1 means it contains
m different species with exactly one member each, while mxN means
there are m different species, and one or more species has more than one
sequence. 
<li>Filter on Method, which is the name of the clustering method (more than one
group of clusters can exist in the database, where each cluster set was built with
a given 'Method'). 
</ul>

<h3>Species</h3>
The multiTCW database was created from one or more singleTCW databases, where each
one is referred to as a species. Hence, each cluster contains sequences from one
or more species.
<p>
Select a set of species to <i>Include</i>, along with setting how many sequences 
from each species must be in the cluster. 
<p>You may also select to exclude clusters that have one or more sequences from the
selected Exclude species set. 
<p>
For both the include and exclude filters, you can choose to apply the sequence limit to 
either all of the All Species selected, or to Any Species selected; in the latter case 
the cluster will be shown if it passes the filter for at least one of the selected species.

<p><b>Example: </b> Select to include species X and species Y, exclude all other species, 
and select Taxa type 2x1. The results will show only clusters 
with two sequences, one from X and one from Y.

<h3>DE members</h3>
BEWARE: this can be a slow query. Make sure to select a method if your database contains
multiple cluster methods; that will speed it up. A progress line will be written to the
terminal for Desktop applications.

<ul>
<li>A cluster must have N species that have at least one member that passes the filters,
where it will be any N of the M total species. If you want all members to pass the filters,
change the "at least 1" to "all" (this is very strict).
<li>Set the Pvalue to the desired value for filtering.
<li>The DE columns are a pair of libraries. Each pair is listed twice, once with no sign and once with "-". The "-" indicates that
the first library of the pair should be less than the second library.
<ul>
<li>Lib1 upregulated compared to lib2, select the Lib1Lib2 pairs.
<li>Lib1 downregulated compared to lib2, select the -Lib1Lib2 pair.
<li>There is NO "either" -- do NOT select Lib1Lib2 and -Lib1Lib2.
</ul>
<li>Select one or more DE columns by highlighting a DE column on the right followed by '<'. 
If more than one DE column is selected, a member must be DE for both.
</ul>
For example, if you have libraries Tip, Root and Zone with DE columns RoTi, RoZo, and TiZo and
you wanted to know what genes have Tip upregulated compared with Root and Zone, you would
select TiZo (for tip > zone) and -RoTi (for root < tip).
 



